Program publications

We look to complete each collaborative project with a publication. In most cases, all of the fellows are included as authors, reflecting the highly collaborative nature of bioinformatic analysis conducted within the Program.

Fellow-initiated projects

  1. We developed an R package for genome interval analysis in R and RStudio (Riemondy et al. 2017).

  2. We developed a method to isolate transcriptome subsets from pooled single-cell RNA sequencing libraries (K. A. Riemondy, Ransom, et al. 2018).

Collaborative projects

  1. With Rachel Zemans’ group, we analyzed single cell RNA-Seq data from a lung injury model to characterize the transdifferentiation of type II alveolar cells to type I cells (Riemondy et al. 2019).

  2. With Craig Jordan’s group, we analyzed single cell RNA-Seq data from AML patients treated with chemotherapy to monitor alterations in AML populations (Pollyea et al. 2018).

  3. With Sandy Martin’s group, we discovered widespread RNA A-to-I editing in the hibernating mammalian brain (K. A. Riemondy, Gillen, et al. 2018).

  4. With Laurent Gapin’s group, we characterized gene expression profiles of invariant Natural Killer T cell populations (Tuttle et al. 2018).

  5. With Sandy Martin’s group, we characterized mRNA splicing and alternative polyadenylation in the hibernating mammalian brain (Gillen et al., forthcoming).

  6. With Matt Burchill and Beth Tamburini’s group, we analyzed single cell RNA-Seq data from chronic liver disease gain more insights into the biology of a rare lymphatic endothelial cell type in the liver. (Tamburini et al., forthcoming)

Gillen, A., R. Fu, K. A. Riemondy, J. R. Hesselberth, and S. L. Martin. Forthcoming. “MRNA Processing in the Brain of a Heterothermic Mammal During Hibernation.”

Pollyea, D. A., B. M. Stevens, C. L. Jones, A. Winters, S. Pei, M. Minhajuddin, A. D’Alessandro, et al. 2018. “Venetoclax with Azacitidine Disrupts Energy Metabolism and Targets Leukemia Stem Cells in Patients with Acute Myeloid Leukemia.” Nat. Med. 24 (12): 1859–66. http://pubmed.com/30420752.

Riemondy, K. A., A. E. Gillen, E. A. White, L. K. Bogren, J. R. Hesselberth, and S. L. Martin. 2018. “Dynamic Temperature-Sensitive a-to-I Rna Editing in the Brain of a Heterothermic Mammal During Hibernation.” RNA 24 (11): 1481–95. http://pubmed.com/30065024.

Riemondy, K. A., N. L. Jansing, P. Jiang, E. F. Redente, A. E. Gillen, R. Fu, A. J. Miller, et al. 2019. “Single Cell Rna Sequencing Identifies Tgf-β as a Key Regenerative Cue Following Lps-Induced Lung Injury.” JCI Insight 5 (March). http://pubmed.com/30913038.

Riemondy, K. A., M. Ransom, C. Alderman, A. E. Gillen, R. Fu, J. Finlay-Schultz, G. D. Kirkpatrick, et al. 2018. “Recovery and Analysis of Transcriptome Subsets from Pooled Single-Cell Rna-Seq Libraries.” Nucleic Acids Res., November. http://pubmed.com/30496484.

Riemondy, K. A., R. M. Sheridan, A. Gillen, Y. Yu, C. G. Bennett, and J. R. Hesselberth. 2017. “Valr: Reproducible Genome Interval Analysis in R.” F1000Res 6: 1025. http://pubmed.com/28751969.

Tamburini, B. A., J. M. Finlon, Gillen A. E., M. S. Kriss, K. A. Riemondy, R. Fu, R. Schuyler, Hesselberth J. R., H. R. Rosen, and M. A. Burchill. Forthcoming. “Chronic Liver Disease in Humans Causes Expansion and Differentiation of Liver Lymphatic Endothelial Cells.”

Tuttle, K. D., S. H. Krovi, J. Zhang, R. Bedel, L. Harmacek, L. K. Peterson, L. L. Dragone, et al. 2018. “TCR Signal Strength Controls Thymic Differentiation of iNKT Cell Subsets.” Nat Commun 9 (1): 2650. http://pubmed.com/29985393.